I've been rooting around for more details, and finally turned up something that might actually be relevant to cycling (and not just train anoraks).
From what I read, currently the "up" Fort William portion of the Highland Sleeper (i.e. the bit heading for London) gets to Edinburgh to be joined with the Inverness and Aberdeen portions. Each part is 6 cars long; 4 sleeper cars, a lounge/guards van and a seated passenger van. However there is a 16 carriage limit for the consist heading south from Edinburgh. This means that 2 cars are detached from the Fort William portion so the lounge, seated passengers and outsize luggage (i.e. bikes) have to be transferred to the Aberdeen portion of the train.
Apparently the new arrangements only have 3 sleeper cars therefore a 15 car train in total and mean that this manoeuvre will no longer be necessary and bikes can stay in place all the way from Fort William to London.
Also, the inconvenient stop in Glasgow at Westerton on the western outskirts is to be replaced by one at Queen Street Low Level. Useful, as the morning down train (to Fort William) is actually a timetabled service for early morning Hillwalkers and those heading to Mallaig for early ferries and the up train is the only train out of Fort William late at night to Glasgow and Edinburgh that can meet trains serving the small isles ferries and evening sailing from Armadale.
I have also read that due to rebuilding of Euston (and also if HS2 goes there) that the Sleeper may have to relocate, probably to Waterloo.